diff --git a/README.md b/README.md index bd7642d..41219b9 100644 --- a/README.md +++ b/README.md @@ -1 +1 @@ -# lie_topology \ No newline at end of file +# mdstudio_topology \ No newline at end of file diff --git a/lie_topology/parsers/topology/__init__.py b/lie_topology/parsers/topology/__init__.py deleted file mode 100644 index 64812ff..0000000 --- a/lie_topology/parsers/topology/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from lie_topology.parsers.topology.read_mdtop import read_mdtop \ No newline at end of file diff --git a/lie_topology/__init__.py b/mdstudio_topology/__init__.py similarity index 100% rename from lie_topology/__init__.py rename to mdstudio_topology/__init__.py diff --git a/lie_topology/__main__.py b/mdstudio_topology/__main__.py similarity index 80% rename from lie_topology/__main__.py rename to mdstudio_topology/__main__.py index 6acfc67..e95ec2c 100644 --- a/lie_topology/__main__.py +++ b/mdstudio_topology/__main__.py @@ -3,24 +3,24 @@ import yaml -from lie_topology.molecule.molecule import Molecule -from lie_topology.molecule.blueprint import Blueprint -from lie_topology.molecule.structure import Structure -from lie_topology.parsers.cnfParser import ParseCnf -from lie_topology.parsers.pdbParser import ParsePdb -from lie_topology.parsers.groParser import ParseGro -from lie_topology.parsers.sdfParser import ParseSdf -from lie_topology.parsers.mol2Parser import ParseMol2 -from lie_topology.parsers.mdtopParser import ParseMdtop -from lie_topology.parsers.mdmtbParser import ParseMDMtb +from mdstudio_topology.molecule.molecule import Molecule +from mdstudio_topology.molecule.blueprint import Blueprint +from mdstudio_topology.molecule.structure import Structure +from mdstudio_topology.parsers.cnfParser import ParseCnf +from mdstudio_topology.parsers.pdbParser import ParsePdb +from mdstudio_topology.parsers.groParser import ParseGro +from mdstudio_topology.parsers.sdfParser import ParseSdf +from mdstudio_topology.parsers.mol2Parser import ParseMol2 +from mdstudio_topology.parsers.mdtopParser import ParseMdtop +from mdstudio_topology.parsers.mdmtbParser import ParseMDMtb -from lie_topology.utilities.make_topology import MakeSequence +from mdstudio_topology.utilities.make_topology import MakeSequence -from lie_topology.writers.cnfWriter import WriteCnf -from lie_topology.writers.gromosTopologyWriter import WriteGromosTopology +from mdstudio_topology.writers.cnfWriter import WriteCnf +from mdstudio_topology.writers.gromosTopologyWriter import WriteGromosTopology -from lie_topology.forcefield.physconst import PhysicalConstants -from lie_topology.molecule.crystal import BoxVectorsToLattice, LatticeToBoxVectors +from mdstudio_topology.forcefield.physconst import PhysicalConstants +from mdstudio_topology.molecule.crystal import BoxVectorsToLattice, LatticeToBoxVectors def WriteSimJson( forcefield, coordinates ): @@ -108,7 +108,7 @@ def main(): def main(): # test atom schema - with open("lie_topology/schemas/resources/atom.v1.json", 'r') as ifs: + with open("mdstudio_topology/schemas/resources/atom.v1.json", 'r') as ifs: schema = json.load(ifs) @@ -116,7 +116,7 @@ def main(): jsonschema.validate( test_atom, schema) - with open("lie_topology/schemas/resources/bond.v1.json", 'r') as ifs: + with open("mdstudio_topology/schemas/resources/bond.v1.json", 'r') as ifs: schema = json.load(ifs) @@ -127,7 +127,7 @@ def main(): """ from mdstudio.runner import main -from lie_topology.application import TopologyComponent +from mdstudio_topology.application import TopologyComponent if __name__ == '__main__': - main(TopologyComponent) \ No newline at end of file + main(TopologyComponent) diff --git a/lie_topology/application.py b/mdstudio_topology/application.py similarity index 99% rename from lie_topology/application.py rename to mdstudio_topology/application.py index 69008df..8d34fa9 100644 --- a/lie_topology/application.py +++ b/mdstudio_topology/application.py @@ -70,7 +70,5 @@ def is_debug(self): self.log.info('debug_sytem {sys:s}', sys=str(response["system"])) - def report_delay(self, direction, delay): self.log.info('{direction:>20} delay: {delay:>8.2f} ms', direction=direction, delay=delay.total_seconds() * 1000) - diff --git a/lie_topology/core/__init__.py b/mdstudio_topology/core/__init__.py similarity index 100% rename from lie_topology/core/__init__.py rename to mdstudio_topology/core/__init__.py diff --git a/lie_topology/core/atom.py b/mdstudio_topology/core/atom.py similarity index 100% rename from lie_topology/core/atom.py rename to mdstudio_topology/core/atom.py diff --git a/lie_topology/core/group.py b/mdstudio_topology/core/group.py similarity index 92% rename from lie_topology/core/group.py rename to mdstudio_topology/core/group.py index c117419..da895b8 100644 --- a/lie_topology/core/group.py +++ b/mdstudio_topology/core/group.py @@ -2,7 +2,7 @@ from collections import OrderedDict -from lie_topology.core.molecule import Molecule +from mdstudio_topology.core.molecule import Molecule class Group(object): diff --git a/lie_topology/core/io/__init__.py b/mdstudio_topology/core/io/__init__.py similarity index 100% rename from lie_topology/core/io/__init__.py rename to mdstudio_topology/core/io/__init__.py diff --git a/lie_topology/core/io/yaml/__init__.py b/mdstudio_topology/core/io/yaml/__init__.py similarity index 100% rename from lie_topology/core/io/yaml/__init__.py rename to mdstudio_topology/core/io/yaml/__init__.py diff --git a/lie_topology/core/io/yaml/yaml_ext.py b/mdstudio_topology/core/io/yaml/yaml_ext.py similarity index 100% rename from lie_topology/core/io/yaml/yaml_ext.py rename to mdstudio_topology/core/io/yaml/yaml_ext.py diff --git a/lie_topology/core/jsonEncoder.py b/mdstudio_topology/core/jsonEncoder.py similarity index 100% rename from lie_topology/core/jsonEncoder.py rename to mdstudio_topology/core/jsonEncoder.py diff --git a/lie_topology/core/molecule.py b/mdstudio_topology/core/molecule.py similarity index 97% rename from lie_topology/core/molecule.py rename to mdstudio_topology/core/molecule.py index 0544a95..ae8fcb1 100644 --- a/lie_topology/core/molecule.py +++ b/mdstudio_topology/core/molecule.py @@ -2,7 +2,7 @@ from collections import OrderedDict -from lie_topology.core.atom import Atom +from mdstudio_topology.core.atom import Atom class Molecule(object): diff --git a/lie_topology/core/system.py b/mdstudio_topology/core/system.py similarity index 85% rename from lie_topology/core/system.py rename to mdstudio_topology/core/system.py index ad903a9..5cfd17e 100644 --- a/lie_topology/core/system.py +++ b/mdstudio_topology/core/system.py @@ -2,8 +2,8 @@ from collections import OrderedDict -from lie_topology.core.group import Group -from lie_topology.core.uuid import UUIDGenerator +from mdstudio_topology.core.group import Group +from mdstudio_topology.core.uuid import UUIDGenerator class System(object): diff --git a/lie_topology/core/tokenizer.py b/mdstudio_topology/core/tokenizer.py similarity index 100% rename from lie_topology/core/tokenizer.py rename to mdstudio_topology/core/tokenizer.py diff --git a/lie_topology/core/topology/__init__.py b/mdstudio_topology/core/topology/__init__.py similarity index 100% rename from lie_topology/core/topology/__init__.py rename to mdstudio_topology/core/topology/__init__.py diff --git a/lie_topology/core/topology/nodes.py b/mdstudio_topology/core/topology/nodes.py similarity index 100% rename from lie_topology/core/topology/nodes.py rename to mdstudio_topology/core/topology/nodes.py diff --git a/lie_topology/core/uuid.py b/mdstudio_topology/core/uuid.py similarity index 100% rename from lie_topology/core/uuid.py rename to mdstudio_topology/core/uuid.py diff --git a/lie_topology/data/cnf/M01.g96 b/mdstudio_topology/data/cnf/M01.g96 similarity index 100% rename from lie_topology/data/cnf/M01.g96 rename to mdstudio_topology/data/cnf/M01.g96 diff --git a/lie_topology/data/cnf/md_fX_apixaban_1.cnf b/mdstudio_topology/data/cnf/md_fX_apixaban_1.cnf similarity index 100% rename from lie_topology/data/cnf/md_fX_apixaban_1.cnf rename to mdstudio_topology/data/cnf/md_fX_apixaban_1.cnf diff --git a/lie_topology/data/cnf/renumber.sh b/mdstudio_topology/data/cnf/renumber.sh similarity index 100% rename from lie_topology/data/cnf/renumber.sh rename to mdstudio_topology/data/cnf/renumber.sh diff --git a/lie_topology/data/gro/run1_combined_pbc.gro b/mdstudio_topology/data/gro/run1_combined_pbc.gro similarity index 100% rename from lie_topology/data/gro/run1_combined_pbc.gro rename to mdstudio_topology/data/gro/run1_combined_pbc.gro diff --git a/lie_topology/data/gtop/ala_ala_ala.gtop b/mdstudio_topology/data/gtop/ala_ala_ala.gtop similarity index 100% rename from lie_topology/data/gtop/ala_ala_ala.gtop rename to mdstudio_topology/data/gtop/ala_ala_ala.gtop diff --git a/lie_topology/data/gtop/ala_cys_ala_cys_ala.gtop b/mdstudio_topology/data/gtop/ala_cys_ala_cys_ala.gtop similarity index 100% rename from lie_topology/data/gtop/ala_cys_ala_cys_ala.gtop rename to mdstudio_topology/data/gtop/ala_cys_ala_cys_ala.gtop diff --git a/lie_topology/data/ifp/2016H66.ifp b/mdstudio_topology/data/ifp/2016H66.ifp similarity index 100% rename from lie_topology/data/ifp/2016H66.ifp rename to mdstudio_topology/data/ifp/2016H66.ifp diff --git a/lie_topology/data/ifp/54a7.ifp b/mdstudio_topology/data/ifp/54a7.ifp similarity index 100% rename from lie_topology/data/ifp/54a7.ifp rename to mdstudio_topology/data/ifp/54a7.ifp diff --git a/lie_topology/data/md_top/54a7.aatop b/mdstudio_topology/data/md_top/54a7.aatop similarity index 100% rename from lie_topology/data/md_top/54a7.aatop rename to mdstudio_topology/data/md_top/54a7.aatop diff --git a/lie_topology/data/md_top/54a7.mdtop b/mdstudio_topology/data/md_top/54a7.mdtop similarity index 100% rename from lie_topology/data/md_top/54a7.mdtop rename to mdstudio_topology/data/md_top/54a7.mdtop diff --git a/lie_topology/data/md_top/54a7mtb_to_aatop.py b/mdstudio_topology/data/md_top/54a7mtb_to_aatop.py similarity index 93% rename from lie_topology/data/md_top/54a7mtb_to_aatop.py rename to mdstudio_topology/data/md_top/54a7mtb_to_aatop.py index d32edea..4b66c4f 100644 --- a/lie_topology/data/md_top/54a7mtb_to_aatop.py +++ b/mdstudio_topology/data/md_top/54a7mtb_to_aatop.py @@ -29,15 +29,15 @@ import json import numpy as np -from lie_topology.common.tokenizer import Tokenizer -from lie_topology.common.exception import LieTopologyException -from lie_topology.molecule.molecule import Molecule -from lie_topology.molecule.bond import Bond -from lie_topology.molecule.angle import Angle -from lie_topology.molecule.dihedral import Dihedral -from lie_topology.molecule.improper import Improper -from lie_topology.molecule.vsite import InPlaneSite -from lie_topology.molecule.reference import AtomReference +from mdstudio_topology.common.tokenizer import Tokenizer +from mdstudio_topology.common.exception import LieTopologyException +from mdstudio_topology.molecule.molecule import Molecule +from mdstudio_topology.molecule.bond import Bond +from mdstudio_topology.molecule.angle import Angle +from mdstudio_topology.molecule.dihedral import Dihedral +from mdstudio_topology.molecule.improper import Improper +from mdstudio_topology.molecule.vsite import InPlaneSite +from mdstudio_topology.molecule.reference import AtomReference def _GenAatopRef( solute, index ): diff --git a/lie_topology/data/md_top/forcefield.mdtop b/mdstudio_topology/data/md_top/forcefield.mdtop similarity index 100% rename from lie_topology/data/md_top/forcefield.mdtop rename to mdstudio_topology/data/md_top/forcefield.mdtop diff --git a/lie_topology/data/md_top/residues.aatop b/mdstudio_topology/data/md_top/residues.aatop similarity index 100% rename from lie_topology/data/md_top/residues.aatop rename to mdstudio_topology/data/md_top/residues.aatop diff --git a/lie_topology/data/mol2/BHC2.mol2 b/mdstudio_topology/data/mol2/BHC2.mol2 similarity index 100% rename from lie_topology/data/mol2/BHC2.mol2 rename to mdstudio_topology/data/mol2/BHC2.mol2 diff --git a/lie_topology/data/mtb/1007.all.mtb b/mdstudio_topology/data/mtb/1007.all.mtb similarity index 100% rename from lie_topology/data/mtb/1007.all.mtb rename to mdstudio_topology/data/mtb/1007.all.mtb diff --git a/lie_topology/data/mtb/2016H66_pept.mtb b/mdstudio_topology/data/mtb/2016H66_pept.mtb similarity index 100% rename from lie_topology/data/mtb/2016H66_pept.mtb rename to mdstudio_topology/data/mtb/2016H66_pept.mtb diff --git a/lie_topology/data/mtb/54a7.mtb b/mdstudio_topology/data/mtb/54a7.mtb similarity index 100% rename from lie_topology/data/mtb/54a7.mtb rename to mdstudio_topology/data/mtb/54a7.mtb diff --git a/lie_topology/data/mtb/g235.mtb b/mdstudio_topology/data/mtb/g235.mtb similarity index 100% rename from lie_topology/data/mtb/g235.mtb rename to mdstudio_topology/data/mtb/g235.mtb diff --git a/lie_topology/data/mtb/minimal.pept.mtb b/mdstudio_topology/data/mtb/minimal.pept.mtb similarity index 100% rename from lie_topology/data/mtb/minimal.pept.mtb rename to mdstudio_topology/data/mtb/minimal.pept.mtb diff --git a/lie_topology/data/pdb/peptide.pdb b/mdstudio_topology/data/pdb/peptide.pdb similarity index 100% rename from lie_topology/data/pdb/peptide.pdb rename to mdstudio_topology/data/pdb/peptide.pdb diff --git a/lie_topology/data/sdf/BHC2.sdf b/mdstudio_topology/data/sdf/BHC2.sdf similarity index 100% rename from lie_topology/data/sdf/BHC2.sdf rename to mdstudio_topology/data/sdf/BHC2.sdf diff --git a/lie_topology/data/test.seq b/mdstudio_topology/data/test.seq similarity index 100% rename from lie_topology/data/test.seq rename to mdstudio_topology/data/test.seq diff --git a/lie_topology/parsers/__init__.py b/mdstudio_topology/parsers/__init__.py similarity index 100% rename from lie_topology/parsers/__init__.py rename to mdstudio_topology/parsers/__init__.py diff --git a/lie_topology/parsers/cnfParser.py b/mdstudio_topology/parsers/cnfParser.py similarity index 96% rename from lie_topology/parsers/cnfParser.py rename to mdstudio_topology/parsers/cnfParser.py index c12251f..a841ac7 100644 --- a/lie_topology/parsers/cnfParser.py +++ b/mdstudio_topology/parsers/cnfParser.py @@ -30,11 +30,11 @@ from copy import deepcopy -from lie_topology.core.tokenizer import Tokenizer -from lie_topology.core.structure import Structure, Time -from lie_topology.core.topology import Topology -from lie_topology.core.crystal import Lattice -from lie_topology.core.group import Group +from mdstudio_topology.core.tokenizer import Tokenizer +from mdstudio_topology.core.structure import Structure, Time +from mdstudio_topology.core.topology import Topology +from mdstudio_topology.core.crystal import Lattice +from mdstudio_topology.core.group import Group def _AppendTopological( activeTopology, resNum, resName, atomName, atomNum ): diff --git a/mdstudio_topology/parsers/topology/__init__.py b/mdstudio_topology/parsers/topology/__init__.py new file mode 100644 index 0000000..dce5a06 --- /dev/null +++ b/mdstudio_topology/parsers/topology/__init__.py @@ -0,0 +1 @@ +from mdstudio_topology.parsers.topology.read_mdtop import read_mdtop \ No newline at end of file diff --git a/lie_topology/parsers/topology/read_mdtop.py b/mdstudio_topology/parsers/topology/read_mdtop.py similarity index 88% rename from lie_topology/parsers/topology/read_mdtop.py rename to mdstudio_topology/parsers/topology/read_mdtop.py index c836be9..c760d6b 100644 --- a/lie_topology/parsers/topology/read_mdtop.py +++ b/mdstudio_topology/parsers/topology/read_mdtop.py @@ -1,7 +1,7 @@ from lie_graph import GraphAxis -from lie_topology.core.io.yaml.yaml_ext import ordered_load -from lie_topology.core.topology.nodes import TopologyNode +from mdstudio_topology.core.io.yaml.yaml_ext import ordered_load +from mdstudio_topology.core.topology.nodes import TopologyNode def read_meta_data(ff_definitions, ff_graph): diff --git a/lie_topology/schemas/endpoints/structure-request.v1.json b/mdstudio_topology/schemas/endpoints/structure-request.v1.json similarity index 100% rename from lie_topology/schemas/endpoints/structure-request.v1.json rename to mdstudio_topology/schemas/endpoints/structure-request.v1.json diff --git a/lie_topology/schemas/endpoints/structure-response.v1.json b/mdstudio_topology/schemas/endpoints/structure-response.v1.json similarity index 100% rename from lie_topology/schemas/endpoints/structure-response.v1.json rename to mdstudio_topology/schemas/endpoints/structure-response.v1.json diff --git a/lie_topology/schemas/endpoints/tti.v1.json b/mdstudio_topology/schemas/endpoints/tti.v1.json similarity index 100% rename from lie_topology/schemas/endpoints/tti.v1.json rename to mdstudio_topology/schemas/endpoints/tti.v1.json diff --git a/lie_topology/schemas/endpoints/tto.v1.json b/mdstudio_topology/schemas/endpoints/tto.v1.json similarity index 100% rename from lie_topology/schemas/endpoints/tto.v1.json rename to mdstudio_topology/schemas/endpoints/tto.v1.json diff --git a/lie_topology/schemas/resources/angle.v1.json b/mdstudio_topology/schemas/resources/angle.v1.json similarity index 100% rename from lie_topology/schemas/resources/angle.v1.json rename to mdstudio_topology/schemas/resources/angle.v1.json diff --git a/lie_topology/schemas/resources/angleType.v1.json b/mdstudio_topology/schemas/resources/angleType.v1.json similarity index 100% rename from lie_topology/schemas/resources/angleType.v1.json rename to mdstudio_topology/schemas/resources/angleType.v1.json diff --git a/lie_topology/schemas/resources/atom.v1.json b/mdstudio_topology/schemas/resources/atom.v1.json similarity index 100% rename from lie_topology/schemas/resources/atom.v1.json rename to mdstudio_topology/schemas/resources/atom.v1.json diff --git a/lie_topology/schemas/resources/atomReference.v1.json b/mdstudio_topology/schemas/resources/atomReference.v1.json similarity index 100% rename from lie_topology/schemas/resources/atomReference.v1.json rename to mdstudio_topology/schemas/resources/atomReference.v1.json diff --git a/lie_topology/schemas/resources/bond.v1.json b/mdstudio_topology/schemas/resources/bond.v1.json similarity index 100% rename from lie_topology/schemas/resources/bond.v1.json rename to mdstudio_topology/schemas/resources/bond.v1.json diff --git a/lie_topology/schemas/resources/bondType.v1.json b/mdstudio_topology/schemas/resources/bondType.v1.json similarity index 100% rename from lie_topology/schemas/resources/bondType.v1.json rename to mdstudio_topology/schemas/resources/bondType.v1.json diff --git a/lie_topology/schemas/resources/dihedral.v1.json b/mdstudio_topology/schemas/resources/dihedral.v1.json similarity index 100% rename from lie_topology/schemas/resources/dihedral.v1.json rename to mdstudio_topology/schemas/resources/dihedral.v1.json diff --git a/lie_topology/schemas/resources/dihedralType.v1.json b/mdstudio_topology/schemas/resources/dihedralType.v1.json similarity index 100% rename from lie_topology/schemas/resources/dihedralType.v1.json rename to mdstudio_topology/schemas/resources/dihedralType.v1.json diff --git a/lie_topology/schemas/resources/exclusion.v1.json b/mdstudio_topology/schemas/resources/exclusion.v1.json similarity index 100% rename from lie_topology/schemas/resources/exclusion.v1.json rename to mdstudio_topology/schemas/resources/exclusion.v1.json diff --git a/lie_topology/schemas/resources/group.v1.json b/mdstudio_topology/schemas/resources/group.v1.json similarity index 100% rename from lie_topology/schemas/resources/group.v1.json rename to mdstudio_topology/schemas/resources/group.v1.json diff --git a/lie_topology/schemas/resources/improper.v1.json b/mdstudio_topology/schemas/resources/improper.v1.json similarity index 100% rename from lie_topology/schemas/resources/improper.v1.json rename to mdstudio_topology/schemas/resources/improper.v1.json diff --git a/lie_topology/schemas/resources/improperType.v1.json b/mdstudio_topology/schemas/resources/improperType.v1.json similarity index 100% rename from lie_topology/schemas/resources/improperType.v1.json rename to mdstudio_topology/schemas/resources/improperType.v1.json diff --git a/lie_topology/schemas/resources/molecule.v1.json b/mdstudio_topology/schemas/resources/molecule.v1.json similarity index 100% rename from lie_topology/schemas/resources/molecule.v1.json rename to mdstudio_topology/schemas/resources/molecule.v1.json diff --git a/lie_topology/schemas/resources/reference.v1.json b/mdstudio_topology/schemas/resources/reference.v1.json similarity index 100% rename from lie_topology/schemas/resources/reference.v1.json rename to mdstudio_topology/schemas/resources/reference.v1.json diff --git a/lie_topology/schemas/resources/system.v1.json b/mdstudio_topology/schemas/resources/system.v1.json similarity index 100% rename from lie_topology/schemas/resources/system.v1.json rename to mdstudio_topology/schemas/resources/system.v1.json diff --git a/lie_topology/schemas/resources/vec3.v1.json b/mdstudio_topology/schemas/resources/vec3.v1.json similarity index 100% rename from lie_topology/schemas/resources/vec3.v1.json rename to mdstudio_topology/schemas/resources/vec3.v1.json diff --git a/lie_topology/schemas/settings.json b/mdstudio_topology/schemas/settings.json similarity index 100% rename from lie_topology/schemas/settings.json rename to mdstudio_topology/schemas/settings.json diff --git a/settings.yml b/settings.yml index c620980..e771fd6 100644 --- a/settings.yml +++ b/settings.yml @@ -1,3 +1,3 @@ static: vendor: mdgroup - component: lie_topology \ No newline at end of file + component: mdstudio_topology \ No newline at end of file diff --git a/setup.py b/setup.py index 5815e62..c275b54 100644 --- a/setup.py +++ b/setup.py @@ -1,11 +1,11 @@ #! /usr/bin/env python # -*- coding: utf-8 -*- -# package: lie_docking +# package: mdstudio_topology # file: setup.py # -# Part of ‘lie_docking’, a package providing molecular docking functionality -# for the LIEStudio package. +# Part of ‘mdstudio_topology’, a package providing component wrapping +# topology parsers and writers for theMDStudio package. # # Copyright © 2018 K.M.Visscher, VU University Amsterdam, the Netherlands # @@ -24,7 +24,7 @@ from setuptools import setup, find_packages -distribution_name = 'lie_topology' +distribution_name = 'mdstudio_topology' setup( name=distribution_name, @@ -32,12 +32,12 @@ description='MDStudio component wrapping topology parsers and writers', author='Koen M. Visscher, VU University, Amsterdam, The Netherlands', author_email=['k.m.visscher@vu.nl'], - url='https://github.com/MD-Studio/lie_topology.git', + url='https://github.com/MD-Studio/MDStudio_topology.git', license='Apache Software License 2.0', - keywords='MDStudio molecular simulation', + keywords='MDStudio molecular simulation topology', platforms=['Any'], packages=find_packages(), - package_data={'lie_topology': ['data/*']}, + package_data={'mdstudio_topology': ['data/*']}, py_modules=[distribution_name], install_requires=['mdstudio', 'numpy','lie_graph'], include_package_data=False, diff --git a/tests/__main__.py b/tests/__main__.py index e88f227..4cf892b 100644 --- a/tests/__main__.py +++ b/tests/__main__.py @@ -4,7 +4,7 @@ from lie_graph import GraphAxis from enum import Enum -from lie_topology.parsers.topology import read_mdtop +from mdstudio_topology.parsers.topology import read_mdtop class NodeType(Enum): Atom = 1 @@ -20,7 +20,7 @@ class EdgeType(Enum): def verify_graph(): - print('running debug version of lie_topology') + print('running debug version of mdstudio_topology') system = GraphAxis() # testing a molecule graph setup